Difference between revisions of "CTS2 RDF Plugin"

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(Created page with "== CTS2 REST Services == === CodeSystemCatalogQuery === * Query: {{CTS2_REST_base}}codesystems ** Query with 'about' filter: {{CTS2_REST_base}}codesystems?matchvalue=oid&filt...")
 
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=== CodeSystemCatalogQuery ===
 
=== CodeSystemCatalogQuery ===
 
* Query: {{CTS2_REST_base}}codesystems
 
* Query: {{CTS2_REST_base}}codesystems
−
** Query with 'about' filter: {{CTS2_REST_base}}codesystems?matchvalue=oid&filtercomponent=about
+
** Query with 'about' filter: {{CTS2_RDF_base}}codesystems?matchvalue=oid&filtercomponent=about
−
** Query with 'name' filter: {{CTS2_REST_base}}codesystems?matchvalue=nci&filtercomponent=resourceName
+
** Query with 'name' filter: {{CTS2_RDF_base}}codesystems?matchvalue=nci&filtercomponent=resourceName
−
** Query with 'description' filter: {{CTS2_REST_base}}codesystems?matchvalue=databases&filtercomponent=resourceSynopsis
+
** Query with 'description' filter: {{CTS2_RDF_base}}codesystems?matchvalue=databases&filtercomponent=resourceSynopsis
−
** Query with 'keyword' filter: {{CTS2_REST_base}}codesystems?matchvalue=100&filtercomponent=keyword
+
** Query with 'keyword' filter: {{CTS2_RDF_base}}codesystems?matchvalue=100&filtercomponent=keyword
−
** Query with 'bioportalId' filter: {{CTS2_REST_base}}codesystems?matchvalue=1007&filtercomponent=ontologyId&referencetype=property
+
** Query with 'bioportalId' filter: {{CTS2_RDF_base}}codesystems?matchvalue=1007&filtercomponent=ontologyId&referencetype=property
 
** ('contains' and 'exactmatch' algorithms supported)
 
** ('contains' and 'exactmatch' algorithms supported)
 
* 'Count' via HEAD call
 
* 'Count' via HEAD call
  
 
=== CodeSystemCatalogRead ===
 
=== CodeSystemCatalogRead ===
−
* Read by name: {{CTS2_REST_base}}codesystem/SNOMEDCT
+
* Read by name: {{CTS2_RDF_base}}codesystem/SNOMEDCT
−
* Read by uri: {{CTS2_REST_base}}codesystembyuri?uri=http://purl.bioontology.org/ontology/SNOMEDCT
+
* Read by uri: {{CTS2_RDF_base}}codesystembyuri?uri=http://purl.bioontology.org/ontology/SNOMEDCT
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== CodeSystemCatalogVersionQuery ===
 
=== CodeSystemCatalogVersionQuery ===
−
* Query: {{CTS2_REST_base}}codesystemversions
+
* Query: {{CTS2_RDF_base}}codesystemversions
−
* Query code system versions of code system: {{CTS2_REST_base}}codesystem/SNOMEDCT/versions
+
* Query code system versions of code system: {{CTS2_RDF_base}}codesystem/SNOMEDCT/versions
−
** Query with 'about' filter: {{CTS2_REST_base}}codesystemversions?matchvalue=oid&filtercomponent=about
+
** Query with 'about' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=oid&filtercomponent=about
−
** Query with 'name' filter: {{CTS2_REST_base}}codesystemversions?matchvalue=nci&filtercomponent=resourceName
+
** Query with 'name' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=nci&filtercomponent=resourceName
−
** Query with 'description' filter: {{CTS2_REST_base}}codesystemversions?matchvalue=anatomy&filtercomponent=resourceSynopsis
+
** Query with 'description' filter: {{CTS2_RDF_base}}codesystemversions?matchvalue=anatomy&filtercomponent=resourceSynopsis
 
** ('contains' and 'exactmatch' algorithms supported)
 
** ('contains' and 'exactmatch' algorithms supported)
 
* 'Count' via HEAD call
 
* 'Count' via HEAD call
  
 
=== CodeSystemVersionCatalogRead ===
 
=== CodeSystemVersionCatalogRead ===
−
* Read by name: {{CTS2_REST_base}}codesystem/LNC/version/LNC_226_RRF
+
* Read by name: {{CTS2_RDF_base}}codesystem/LNC/version/LNC_226_RRF
−
* Or OfficialResourceVersionId: {{CTS2_REST_base}}codesystem/LNC/version/226
+
* Or OfficialResourceVersionId: {{CTS2_RDF_base}}codesystem/LNC/version/226
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== EntityDescriptionQuery ===
 
=== EntityDescriptionQuery ===
−
* Query with 'description' {{CTS2_REST_base}}entities?matchvalue=swelling
+
* Query with 'description' {{CTS2_RDF_base}}entities?matchvalue=swelling
−
* Get all entities of code system version: {{CTS2_REST_base}}codesystem/AIR/version/AIR_1993_RRF/entities
+
* Get all entities of code system version: {{CTS2_RDF_base}}codesystem/AIR/version/AIR_1993_RRF/entities
 
* Query entities of code system version with 'keyword' filter: {{CTS2_REST_base}}codesystem/LNC/version/LNC_226_RRF/entities?matchvalue=100
 
* Query entities of code system version with 'keyword' filter: {{CTS2_REST_base}}codesystem/LNC/version/LNC_226_RRF/entities?matchvalue=100
 
** ('contains' and 'exactmatch' algorithms supported)
 
** ('contains' and 'exactmatch' algorithms supported)
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=== EntityDescriptionRead ===
 
=== EntityDescriptionRead ===
−
* Read by name: {{CTS2_REST_base}}codesystem/LNC/version/LNC_226_RRF/entity/LP31957-1
+
* Read by name: {{CTS2_RDF_base}}codesystem/LNC/version/LNC_226_RRF/entity/LP31957-1
 
* Or using CSV OfficialResourceVersionId : {{CTS2_REST_base}}codesystem/LNC/version/226/entity/LP31957-1
 
* Or using CSV OfficialResourceVersionId : {{CTS2_REST_base}}codesystem/LNC/version/226/entity/LP31957-1
 
*: NOTE: Does not support Entity lookup by URI (See notes below)
 
*: NOTE: Does not support Entity lookup by URI (See notes below)
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=== ValueSetCatalogQuery ===
 
=== ValueSetCatalogQuery ===
−
* Query: {{CTS2_REST_base}}valuesets
+
* Query: {{CTS2_RDF_base}}valuesets
−
** Query with 'about' filter: {{CTS2_REST_base}}valuesets?matchvalue=FMA_subset&filtercomponent=about
+
** Query with 'about' filter: {{CTS2_RDF_base}}valuesets?matchvalue=FMA_subset&filtercomponent=about
−
** Query with 'name' filter: {{CTS2_REST_base}}valuesets?matchvalue=set&filtercomponent=resourceName
+
** Query with 'name' filter: {{CTS2_RDF_base}}valuesets?matchvalue=set&filtercomponent=resourceName
−
** Query with 'description' filter: {{CTS2_REST_base}}valuesets?matchvalue=anatomy&filtercomponent=resourceSynopsis
+
** Query with 'description' filter: {{CTS2_RDF_base}}valuesets?matchvalue=anatomy&filtercomponent=resourceSynopsis
−
** Query based on code system restriction: {{CTS2_REST_base}}valuesets?codesystem=SNOMEDCT
+
** Query based on code system restriction: {{CTS2_RDF_base}}valuesets?codesystem=SNOMEDCT
 
** ('contains' and 'exactmatch' algorithms supported)
 
** ('contains' and 'exactmatch' algorithms supported)
 
* 'Count' via HEAD call
 
* 'Count' via HEAD call
  
 
=== ValueSetCatalogRead ===
 
=== ValueSetCatalogRead ===
−
* Read by name: {{CTS2_REST_base}}valueset/SNOMEDCT-MAS
+
* Read by name: {{CTS2_RDF_base}}valueset/SNOMEDCT-MAS
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== ValueSetDefinitionQuery ===
 
=== ValueSetDefinitionQuery ===
−
* Read by name: {{CTS2_REST_base}}valueset/SCTSPA/definitions
+
* Read by name: {{CTS2_RDF_base}}valueset/SCTSPA/definitions
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== ValueSetDefinitionRead ===
 
=== ValueSetDefinitionRead ===
−
* Read by name: {{CTS2_REST_base}}valueset/SCTSPA/definition/42157
+
* Read by name: {{CTS2_RDF_base}}valueset/SCTSPA/definition/42157
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== ValueSetDefinitionResolutionService ===
 
=== ValueSetDefinitionResolutionService ===
−
* Read by name: {{CTS2_REST_base}}valueset/SCTSPA/definition/42157/resolution?resolutiontype=entitydirectory
+
* Read by name: {{CTS2_RDF_base}}valueset/SCTSPA/definition/42157/resolution?resolutiontype=entitydirectory
 
* 'Exists' via HEAD call
 
* 'Exists' via HEAD call
  
 
=== AssociationQuery ===
 
=== AssociationQuery ===
−
* Query 'sourceOf' associations of entity: {{CTS2_REST_base}}codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/entity/100001001/sourceof
+
* Query 'sourceOf' associations of entity: {{CTS2_RDF_base}}codesystem/SNOMEDCT/version/SNOMEDCT_2010_01_31_RRF/entity/100001001/sourceof
−
* Query 'children' associations of entity: {{CTS2_REST_base}}codesystem/MSH/version/MSH_2009_2009_02_13_RRF/entity/D006321/children
+
* Query 'children' associations of entity: {{CTS2_RDF_base}}codesystem/MSH/version/MSH_2009_2009_02_13_RRF/entity/D006321/children
  
 
=== AdvancedAssociationQuery ===
 
=== AdvancedAssociationQuery ===
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* NOTES: Currently only supports direction=FORWARD and depth=1
 
* NOTES: Currently only supports direction=FORWARD and depth=1
  
−
== ISSUES ==
 
−
* URI issues
 
−
* Views as ontologies is problematic
 
−
* Search returns hits back from views. We can restrict the search to only ontologyIds that are ontologies, but that tested to be a 4-5x performance hit on the searc
 
−
* A search will sometimes return results with an 'ontologyId' that doesn't match to anything. For example:
 
−
** <nowiki>http://rest.bioontology.org/bioportal/search/core?apikey=880e5e30-0fa9-4cba-b25f-3069b15577f9</nowiki>
 
−
**: results in:
 
−
<nowiki>
 
−
<searchBean>
 
−
<ontologyVersionId>45952</ontologyVersionId>
 
−
<ontologyId>1634</ontologyId>
 
−
<ontologyDisplayLabel>Infectious DIsease Ontology</ontologyDisplayLabel>
 
−
<recordType>apreferredname</recordType>
 
−
<objectType>individual</objectType>
 
−
<conceptId>http://purl.obolibrary.org/obo/IAO_0000224</conceptId>
 
−
<conceptIdShort>obo:IAO_0000224</conceptIdShort>
 
−
<preferredName>core</preferredName>
 
−
<contents>core</contents>
 
−
</searchBean>
 
−
...
 
−
  </nowiki>
 
−
**: "1634" is not found in the results from http://rest.bioontology.org/bioportal/ontologies?apikey=YourAPIKey
 
−
* No bioportal REST signature to search for an entity based on ontologyVersionId
 
−
* No bioportal REST signation to get an Entity by its URI (or 'fullId') in bioportal
 
−
* No good way to get all entities in the system (can get all of an ontologyId)
 
−
 
−
* Can't get all associations, so we can't do /codesystem/CSNAME/version/VERSION/associations -- there is no efficient way to do this in bioportal.
 
  
 
== SVN ==
 
== SVN ==
 
SVN [http://informatics.mayo.edu/svn/trunk/cts2/impl/cts2-rest/ url]
 
SVN [http://informatics.mayo.edu/svn/trunk/cts2/impl/cts2-rest/ url]

Revision as of 12:01, 1 June 2012

CTS2 REST Services

CodeSystemCatalogQuery

CodeSystemCatalogRead

CodeSystemCatalogVersionQuery

CodeSystemVersionCatalogRead

EntityDescriptionQuery

EntityDescriptionRead

ValueSetCatalogQuery

ValueSetCatalogRead

ValueSetDefinitionQuery

ValueSetDefinitionRead

ValueSetDefinitionResolutionService

AssociationQuery

AdvancedAssociationQuery


SVN

SVN url

Retrieved from "https://www.bioontology.org//mediawiki/index.php?title=CTS2_RDF_Plugin&oldid=12234"